The controversial speakership of John Bercow won an important endorsement when parliament's most senior official announced his retirement with a declaration that the House of Commons is scrutinising the government more effectively than ever.

Sir Robert Rogers, the highly respected clerk of the House of Commons, received a rare round of applause from MPs after Bercow read out his retirement letter, which highlighted the way in which parliament had become more relevant.

But senior figures in Westminster said Rogers, who will retire in August six months short of his 65th birthday, had found it difficult to work with the Speaker. Sources familiar with the Speaker's office describe the atmosphere as tense and unpredictable.

In his letter Rogers made no mention of any difficulties behind the scenes as he wrote graciously of how parliament had been transformed over the past decade. His letter, read out by Bercow, said: "I have been lucky enough to have been involved in most of the innovations in the procedure and business of the house over the last 10 years. Whatever the vicissitudes of parliamentary life and whatever brickbats may be thrown at it, I can truly say that the house now is a more effective scrutineer of the executive and more topical, relevant and independent-minded than I have ever known it."

The remarks by Rogers marked a strong endorsement of the way in which Bercow has tried to strengthen parliament's scrutiny of the government by hauling in ministers to answer urgent parliamentary questions.

This has also made the Commons more relevant to running issues of the day. Ministers regularly brief journalists against Bercow.

Rogers, who has served parliament for the past 42 years, also moved to address criticisms of MPs after the recent expenses scandals. He praised MPs for the way in which they champion vulnerable people. He described MPs as the "last resort of the homeless and hopeless – the people whom society has let down". He added: "This is a worthy calling and should be properly acknowledged and appreciated."